GapMind for catabolism of small carbon sources

 

L-fucose catabolism

Analysis of pathway fucose in 35 genomes

Genome Best path
Acidovorax sp. GW101-3H11 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Azospirillum brasilense Sp245 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Bacteroides thetaiotaomicron VPI-5482 fucP, fucU, fucI, fucK, fucA, tpi, fucO
Burkholderia phytofirmans PsJN BPHYT_RS34250, BPHYT_RS34245, BPHYT_RS34240, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Caulobacter crescentus NA1000 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Cupriavidus basilensis 4G11 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Dechlorosoma suillum PS fucP, fucU, fucI, fucK, fucA, tpi, aldA
Desulfovibrio vulgaris Hildenborough fucP, fucU, fucI, fucK, fucA, tpi, fucO
Desulfovibrio vulgaris Miyazaki F fucP, fucU, fucI, fucK, fucA, tpi, fucO
Dinoroseobacter shibae DFL-12 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Dyella japonica UNC79MFTsu3.2 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Echinicola vietnamensis KMM 6221, DSM 17526 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Escherichia coli BW25113 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Herbaspirillum seropedicae SmR1 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Klebsiella michiganensis M5al fucP, fucU, fucI, fucK, fucA, tpi, aldA
Magnetospirillum magneticum AMB-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Marinobacter adhaerens HP15 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Paraburkholderia bryophila 376MFSha3.1 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Pedobacter sp. GW460-11-11-14-LB5 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Phaeobacter inhibens BS107 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens FW300-N1B4 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens FW300-N2C3 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Pseudomonas fluorescens FW300-N2E2 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens FW300-N2E3 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas fluorescens GW456-L13 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas putida KT2440 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas simiae WCS417 HSERO_RS05250, HSERO_RS05255, HSERO_RS05260, fucU, fucI, fucK, fucA, tpi, aldA
Pseudomonas stutzeri RCH2 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella amazonensis SB2B fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella loihica PV-4 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella oneidensis MR-1 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Shewanella sp. ANA-3 fucP, fucU, fucI, fucK, fucA, tpi, aldA
Sinorhizobium meliloti 1021 SM_b21103, SM_b21104, SM_b21105, SM_b21106, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Sphingomonas koreensis DSMZ 15582 fucP, fucU, fdh, fuconolactonase, fucD, fucDH, KDF-hydrolase
Synechococcus elongatus PCC 7942 fucP, fucU, fucI, fucK, fucA, tpi, aldA

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from May 21 2021. The underlying query database was built on May 21 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory